Cross-posted on the DevShed forum (http://forums.devshed.com/perl-programming-6/replace-push-perl-962230.html) where I provided an answer as to what to fix (although not a complete solution). It is considered polite to mention it when you cross-post in various forums, so as to avoid duplicate work on various parts of the Internet.

If I were to give a solution, it would be very similar to NetWallah's proposal, which has the advantage of not storing a file (which may be very large) into an array in memory.